1
|
Kachingwe G, Carletti F, Adan G, Jäger H, Henrion M, Kampondeni S, Joekes E, Chetcuti K, Swayne O, Heyderman R, Allain T, Mwandumba H, Solomon T, Werring D, Benjamin L. CLINICAL AND RADIOLOGICAL CHARACTERISTICS OF HIV-ASSOCIATED INTRACEREBRAL HAEMORRHAGE IN MALAWI. J Stroke Cerebrovasc Dis 2023. [DOI: 10.1016/j.jstrokecerebrovasdis.2023.107009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
|
2
|
Carey L, Tsidya B, Nkhalema B, Kaimba S, Chetcuti K, Joekes E, Kreuels B, Henrion M, Rylance J. Ultrasound appearance of the kidney among radiology department attendees of a tertiary centre in Malawi. Wellcome Open Res 2023; 7:280. [PMID: 36865368 PMCID: PMC9971658 DOI: 10.12688/wellcomeopenres.18455.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Background: Diagnostic and therapeutic decisions in nephrology in low-resource settings are frequently based on ultrasound assessment of kidney size. An understanding of reference values is critical, particularly given the rise of non-communicable disease and the expanding availability of point-of-care ultrasound. However, there is a paucity of normative data from African populations. We determined estimates of kidney ultrasound measures, including kidney size based on age, sex, and HIV status, among apparently healthy outpatient attendees of Queen Elizabeth Central hospital radiology department, Blantyre, Malawi. Methods: We performed a cross-sectional cohort study of 320 adults attending the radiology department between October 2021 and January 2022. Bilateral kidney ultrasound was performed on all participants using a portable Mindray DP-50 machine and a 5MHz convex probe. The sample was stratified by age, sex, and HIV status. Predictive linear modelling was used to construct reference ranges for kidney size estimating the central 95 percentiles of 252 healthy adults. Exclusion criteria for the healthy sample were known kidney disease, hypertension, diabetes, BMI > 35, heavy alcohol intake, smoking and ultrasonographic abnormalities. Results: There were 162/320 (51%) male participants. The median age was 47 (interquartile range [IQR] 34-59). Among people living with HIV 134/138 (97%) were receiving antiretroviral therapy. Men had larger average kidney sizes: mean 9.68 cm (SD 0.80 cm), compared to 9.46 cm (SD 0.87 cm) in women ( p = 0.01). Average kidney sizes in people living with HIV were not significantly different from those who were HIV-negative, 9.73 cm (SD 0.93 cm) versus 9.58 cm (SD 0.93 cm) ( p = 0.63). Conclusions: This is the first report of the apparently healthy kidney size in Malawi. Predicted kidney size ranges may be used for reference in the clinical assessment of kidney disease in Malawi.
Collapse
Affiliation(s)
- Laura Carey
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK,
| | - Bright Tsidya
- Radiology Department, Queen Elizabeth Central Hospital, Blantyre, Malawi,Malawi College of Health Sciences, Blantyre, Malawi
| | - Bazwell Nkhalema
- Radiology Department, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | | | - Karen Chetcuti
- Kamuzu University of Health Sciences, Blantyre, Malawi,Worldwide Radiology, Liverpool, UK
| | - Elizabeth Joekes
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK,Worldwide Radiology, Liverpool, UK
| | - Benno Kreuels
- Kamuzu University of Health Sciences, Blantyre, Malawi,Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Department of Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Henrion
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jamie Rylance
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| |
Collapse
|
3
|
Carey L, Tsidya B, Nkhalema B, Kaimba S, Chetcuti K, Joekes E, Kreuels B, Henrion M, Rylance J. Ultrasound appearance of the kidney among radiology department attendees of a tertiary centre in Malawi. Wellcome Open Res 2023; 7:280. [PMID: 36865368 PMCID: PMC9971658 DOI: 10.12688/wellcomeopenres.18455.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 11/12/2022] Open
Abstract
Background: Diagnostic and therapeutic decisions in nephrology in low-resource settings are frequently based on ultrasound assessment of kidney size. An understanding of reference values is critical, particularly given the rise of non-communicable disease and the expanding availability of point-of-care ultrasound. However, there is a paucity of normative data from sub-Saharan Africa (SSA). We determined estimates of kidney ultrasound measures, including kidney size based on age, sex, and HIV status, among apparently healthy outpatient attendees of Queen Elizabeth Central hospital radiology department, Blantyre, Malawi. Methods: We performed a cross-sectional cohort study of 320 adults attending the radiology department between October 2021 and January 2022. Bilateral kidney ultrasound was performed on all participants using a portable Mindray DP-50 machine and a 5MHz convex probe. The sample was stratified by age, sex, and HIV status. Predictive linear modelling was used to construct reference ranges for kidney size estimating the central 95 percentiles of 252 healthy adults. Exclusion criteria for the healthy sample were known kidney disease, hypertension, diabetes, BMI > 35, heavy alcohol intake, smoking and ultrasonographic abnormalities. Results: There were 162/320 (51%) male participants. The median age was 47 (interquartile range [IQR] 34-59). Of those whose HIV status was known and positive, 138/308 (45%), 134/138 (97%) were receiving antiretroviral therapy. Men had larger average kidney sizes: mean 9.68 cm (SD 0.80 cm), compared to 9.46 cm (SD 0.87 cm) in women ( p = 0.01). Average kidney sizes in HIV-positive participants were not significantly different from those who were HIV-negative, 9.73 cm (SD 0.93 cm) versus 9.58 cm (SD 0.93 cm) ( p = 0.63). Conclusions: This is the first report of the apparently healthy kidney size in Malawi. Predicted kidney size ranges may be used for reference in the clinical assessment of kidney disease in Malawi.
Collapse
Affiliation(s)
- Laura Carey
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK,
| | - Bright Tsidya
- Radiology Department, Queen Elizabeth Central Hospital, Blantyre, Malawi,Malawi College of Health Sciences, Blantyre, Malawi
| | - Bazwell Nkhalema
- Radiology Department, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | | | - Karen Chetcuti
- Kamuzu University of Health Sciences, Blantyre, Malawi,Worldwide Radiology, Liverpool, UK
| | - Elizabeth Joekes
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK,Worldwide Radiology, Liverpool, UK
| | - Benno Kreuels
- Kamuzu University of Health Sciences, Blantyre, Malawi,Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Department of Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Henrion
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jamie Rylance
- Malawi-Liverpool Wellcome Trust, Blantyre, Malawi,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| |
Collapse
|
4
|
Dale H, Chirwa E, Patel P, Makuta G, Mwakiseghile F, Misiri T, Kadwala I, Mbewe M, Banda H, Silungwe N, Chizani K, Kambiya P, Henrion M, French N, Nyirenda T, Gordon M. Understanding the epidemiology of iNTS disease in Africa in preparation for future iNTS- vaccine studies in endemic countries: Seroepidemiology in Africa of iNTS (SAiNTS) Study Protocol [Version 9.0]. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18054.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: Non-typhoidal Salmonella (NTS) are a major cause of bloodstream infections amongst children in sub-Saharan Africa. A clear understanding of the seroepidemiology and correlates of protection for invasive NTS (iNTS) in relation to key risk factors (malaria, anaemia, malnutrition) in children in Africa is needed to inform strategies for disease control including vaccine implementation. Methodology: The SAiNTS study is a prospective community cohort study with paired serology samples from 2500 children 0-5 years at baseline and three months to measure age-stratified acquisition of lipopolysaccharide (LPS) O-antigen antibody (IgG) and serum bactericidal activity to the main serovars causing iNTS (Salmonella typhimurium and S. enteritidis). Children are selected from mapped and censused randomly selected households in Chikwawa, Malawi; an area with substantial malaria burden. The sampling framework is set within a malaria vaccination (RTS,S/ AS01) phase 4 cluster randomized trial (EPIMAL), allowing exploration of the impact of malaria vaccination on acquisition of immunity to NTS. Data on risk factors for invasive disease: malaria, anaemia and malnutrition as well as indicators of socioeconomic status and water and sanitation, will be collected using rapid diagnostic tests, anthropometry and electronic CRF’s. Stool sample analysis includes NTS culture and pan-Salmonella polymerase chain reaction to assess enteric exposure and biomarkers of environmental enteric dysfunction. Cases with iNTS disease will be followed up for comparison with community controls. Conclusions: The final cohort of 2500 children will allow investigation into the impact of risk factors for iNTS on the acquisition of immunity in children 0-5 years in an endemic setting, including comparisons to partner sero-epidemiology studies in three other sub-Saharan African sites. The data generated will be key to informing iNTS disease control measures including targeted risk factor interventions and vaccine implementation through investigation of correlates of protection and identifying windows of immune susceptibility in at-risk populations.
Collapse
|
5
|
Iroh Tam PY, Chirombo J, Henrion M, Newberry L, Mambule I, Everett D, Mwansambo C, Cunliffe N, French N, Heyderman RS, Bar-Zeev N. Clinical pneumonia in the hospitalised child in Malawi in the post-pneumococcal conjugate vaccine era: a prospective hospital-based observational study. BMJ Open 2022; 12:e050188. [PMID: 35135765 PMCID: PMC8830243 DOI: 10.1136/bmjopen-2021-050188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Assess characteristics of clinical pneumonia after introduction of pneumococcal conjugate vaccine (PCV), by HIV exposure status, in children hospitalised in a governmental hospital in Malawi. METHODS AND FINDINGS We evaluated 1139 children ≤5 years old hospitalised with clinical pneumonia: 101 HIV-exposed, uninfected (HEU) and 1038 HIV-unexposed, uninfected (HUU). Median age was 11 months (IQR 6-20), 59% were male, median mid-upper arm circumference (MUAC) was 14 cm (IQR 13-15) and mean weight-for-height z score was -0.7 (±2.5). The highest Respiratory Index of Severity in Children (RISC) scores were allocated to 10.4% of the overall cohort. Only 45.7% had fever, and 37.2% had at least one danger sign at presentation. The most common clinical features were crackles (54.7%), nasal flaring (53.5%) and lower chest wall indrawing (53.2%). Compared with HUU, HEU children were significantly younger (9 months vs 11 months), with lower mean birth weight (2.8 kg vs 3.0 kg) and MUAC (13.6 cm vs 14.0 cm), had higher prevalence of vomiting (32.7% vs 22.0%), tachypnoea (68.4% vs 49.8%) and highest RISC scores (20.0% vs 9.4%). Five children died (0.4%). However, clinical outcomes were similar for both groups. CONCLUSIONS In this post-PCV setting where prevalence of HIV and malnutrition is high, children hospitalised fulfilling the WHO Integrated Management of Childhood Illness criteria for clinical pneumonia present with heterogeneous features. These vary by HIV exposure status but this does not influence either the frequency of danger signs or mortality. The poor performance of available severity scores in this population and the absence of more specific diagnostics hinder appropriate antimicrobial stewardship and the rational application of other interventions.
Collapse
Affiliation(s)
- Pui-Ying Iroh Tam
- Department of Paediatrics and Child Health, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - James Chirombo
- Statistical Support Unit, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Marc Henrion
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Statistical Support Unit, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Laura Newberry
- Department of Paediatrics and Child Health, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Ivan Mambule
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Dean Everett
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Pathology and Infectious Diseases, Khalifa University, Abu Dhabi, UAE
| | | | - Nigel Cunliffe
- Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Neil French
- Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool Faculty of Health and Life Sciences, Liverpool, UK
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Naor Bar-Zeev
- Department of Paediatrics and Child Health, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, UK
- Global Disease Epidemiology and Control, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| |
Collapse
|
6
|
Patel PD, Patel P, Liang Y, Meiring JE, Misiri T, Mwakiseghile F, Tracy JK, Masesa C, Msuku H, Banda D, Mbewe M, Henrion M, Adetunji F, Simiyu K, Rotrosen E, Birkhold M, Nampota N, Nyirenda OM, Kotloff K, Gmeiner M, Dube Q, Kawalazira G, Laurens MB, Heyderman RS, Gordon MA, Neuzil KM. Safety and Efficacy of a Typhoid Conjugate Vaccine in Malawian Children. N Engl J Med 2021; 385:1104-1115. [PMID: 34525285 PMCID: PMC8202713 DOI: 10.1056/nejmoa2035916] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Typhoid fever caused by multidrug-resistant H58 Salmonella Typhi is an increasing public health threat in sub-Saharan Africa. METHODS We conducted a phase 3, double-blind trial in Blantyre, Malawi, to assess the efficacy of Vi polysaccharide typhoid conjugate vaccine (Vi-TCV). We randomly assigned children who were between 9 months and 12 years of age, in a 1:1 ratio, to receive a single dose of Vi-TCV or meningococcal capsular group A conjugate (MenA) vaccine. The primary outcome was typhoid fever confirmed by blood culture. We report vaccine efficacy and safety outcomes after 18 to 24 months of follow-up. RESULTS The intention-to-treat analysis included 28,130 children, of whom 14,069 were assigned to receive Vi-TCV and 14,061 were assigned to receive the MenA vaccine. Blood culture-confirmed typhoid fever occurred in 12 children in the Vi-TCV group (46.9 cases per 100,000 person-years) and in 62 children in the MenA group (243.2 cases per 100,000 person-years). Overall, the efficacy of Vi-TCV was 80.7% (95% confidence interval [CI], 64.2 to 89.6) in the intention-to-treat analysis and 83.7% (95% CI, 68.1 to 91.6) in the per-protocol analysis. In total, 130 serious adverse events occurred in the first 6 months after vaccination (52 in the Vi-TCV group and 78 in the MenA group), including 6 deaths (all in the MenA group). No serious adverse events were considered by the investigators to be related to vaccination. CONCLUSIONS Among Malawian children 9 months to 12 years of age, administration of Vi-TCV resulted in a lower incidence of blood culture-confirmed typhoid fever than the MenA vaccine. (Funded by the Bill and Melinda Gates Foundation; ClinicalTrials.gov number, NCT03299426.).
Collapse
Affiliation(s)
- Priyanka D Patel
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Pratiksha Patel
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Yuanyuan Liang
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - James E Meiring
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Theresa Misiri
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Felistas Mwakiseghile
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - J Kathleen Tracy
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Clemens Masesa
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Harrison Msuku
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - David Banda
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Maurice Mbewe
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Marc Henrion
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Fiyinfolu Adetunji
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Kenneth Simiyu
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Elizabeth Rotrosen
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Megan Birkhold
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Nginache Nampota
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Osward M Nyirenda
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Karen Kotloff
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Markus Gmeiner
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Queen Dube
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Gift Kawalazira
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Matthew B Laurens
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Robert S Heyderman
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Melita A Gordon
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Kathleen M Neuzil
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| |
Collapse
|
7
|
Iroh Tam P, Arnold SLM, Barrett LK, Chen CR, Conrad TM, Douglas E, Gordon MA, Hebert D, Henrion M, Hermann D, Hollingsworth B, Houpt E, Jere KC, Lindblad R, Love MS, Makhaza L, McNamara CW, Nedi W, Nyirenda J, Operario DJ, Phulusa J, Quinnan GV, Sawyer LA, Thole H, Toto N, Winter A, Van Voorhis WC. Clofazimine for Treatment of Cryptosporidiosis in Human Immunodeficiency Virus Infected Adults: An Experimental Medicine, Randomized, Double-blind, Placebo-controlled Phase 2a Trial. Clin Infect Dis 2021; 73:183-191. [PMID: 32277809 PMCID: PMC8282326 DOI: 10.1093/cid/ciaa421] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/09/2020] [Indexed: 01/01/2023] Open
Abstract
Background We evaluated the efficacy, pharmacokinetics (PK), and safety of clofazimine (CFZ) in patients living with human immunodeficiency virus (HIV) with cryptosporidiosis. Methods We performed a randomized, double-blind, placebo-controlled study. Primary outcomes in part A were reduction in Cryptosporidium shedding, safety, and PK. Primary analysis was according to protocol (ATP). Part B of the study compared CFZ PK in matched individuals living with HIV without cryptosporidiosis. Results Twenty part A and 10 part B participants completed the study ATP. Almost all part A participants had high viral loads and low CD4 counts, consistent with failure of antiretroviral (ARV) therapy. At study entry, the part A CFZ group had higher Cryptosporidium shedding, total stool weight, and more diarrheal episodes compared with the placebo group. Over the inpatient period, compared with those who received placebo, the CFZ group Cryptosporidium shedding increased by 2.17 log2 Cryptosporidium per gram stool (95% upper confidence limit, 3.82), total stool weight decreased by 45.3 g (P = .37), and number of diarrheal episodes increased by 2.32 (P = .87). The most frequent solicited adverse effects were diarrhea, abdominal pain, and malaise. One placebo and 3 CFZ participants died during the study. Plasma levels of CFZ in participants with cryptosporidiosis were 2-fold lower than in part B controls. Conclusions Our findings do not support the efficacy of CFZ for the treatment of cryptosporidiosis in a severely immunocompromised HIV population. However, this trial demonstrates a pathway to assess the therapeutic potential of drugs for cryptosporidiosis treatment. Screening persons living with HIV for diarrhea, and especially Cryptosporidium infection, may identify those failing ARV therapy. Clinical Trials Registration NCT03341767.
Collapse
Affiliation(s)
- Py Iroh Tam
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - S L M Arnold
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - L K Barrett
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | | | - E Douglas
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - M A Gordon
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - M Henrion
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - D Hermann
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - E Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - K C Jere
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - M S Love
- Calibr, La Jolla, California, USA
| | - L Makhaza
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - W Nedi
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - J Nyirenda
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - D J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - J Phulusa
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - H Thole
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - N Toto
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - W C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| |
Collapse
|
8
|
Meiring JE, Laurens MB, Patel P, Patel P, Misiri T, Simiyu K, Mwakiseghile F, Tracy JK, Masesa C, Liang Y, Henrion M, Rotrosen E, Gmeiner M, Heyderman R, Kotloff K, Gordon MA, Neuzil KM. Typhoid Vaccine Acceleration Consortium Malawi: A Phase III, Randomized, Double-blind, Controlled Trial of the Clinical Efficacy of Typhoid Conjugate Vaccine Among Children in Blantyre, Malawi. Clin Infect Dis 2020; 68:S50-S58. [PMID: 30845320 PMCID: PMC6405268 DOI: 10.1093/cid/ciy1103] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Typhoid fever is an acute infection characterized by prolonged fever following the ingestion and subsequent invasion of Salmonella enterica serovar Typhi (S. Typhi), a human-restricted pathogen. The incidence of typhoid fever has been most reported in children 5-15 years of age, but is increasingly recognized in children younger than 5 years old. There has been a recent expansion of multidrug-resistant typhoid fever globally. Prior typhoid vaccines were not suitable for use in the youngest children in countries with a high burden of disease. This study aims to determine the efficacy of a typhoid conjugate vaccine (TCV) that was recently prequalified by the World Health Organization, by testing it in children 9 months through 12 years of age in Blantyre, Malawi. METHODS In this Phase III, individually randomized, controlled, double-blind trial of the clinical efficacy of TCV, 28 000 children 9 months through 12 years of age will be enrolled and randomized in a 1:1 ratio to receive either Vi-TCV or a meningococcal serogroup A conjugate vaccine. A subset of 600 of these children will be further enrolled in an immunogenicity and reactogenicity sub-study to evaluate the safety profile and immune response elicited by Vi-TCV. Recruiting began in February 2018. RESULTS All children will be under passive surveillance for at least 2 years to determine the primary outcome, which is blood culture-confirmed S. Typhi illness. Children enrolled in the immunogenicity and reactogenicity sub-study will have blood drawn before vaccination and at 2 timepoints after vaccination to measure their immune response to vaccination. They will also be followed actively for adverse events and serious adverse events. CONCLUSIONS The introduction of a single-dose, efficacious typhoid vaccine into countries with high burden of disease or significant antimicrobial resistance could have a dramatic impact, protecting children from infection and reducing antimicrobial usage and associated health inequity in the world's poorest places. This trial, the first of a TCV in Africa, seeks to demonstrate the impact and programmatic use of TCVs within an endemic setting. CLINICAL TRIALS REGISTRATION NCT03299426.
Collapse
Affiliation(s)
- James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, Oxford University, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Pratiksha Patel
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Priyanka Patel
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Theresa Misiri
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kenneth Simiyu
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | | | - J Kathleen Tracy
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Clemens Masesa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Yuanyuan Liang
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Marc Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Elizabeth Rotrosen
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Markus Gmeiner
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Division of Infection and Immunity, University College London, United Kingdom
| | - Karen Kotloff
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| |
Collapse
|
9
|
Johansson M, Carreras-Torres R, Scelo G, Purdue MP, Mariosa D, Muller DC, Timpson NJ, Haycock PC, Brown KM, Wang Z, Ye Y, Hofmann JN, Foll M, Gaborieau V, Machiela MJ, Colli LM, Li P, Garnier JG, Blanche H, Boland A, Burdette L, Prokhortchouk E, Skryabin KG, Yeager M, Radojevic-Skodric S, Ognjanovic S, Foretova L, Holcatova I, Janout V, Mates D, Mukeriya A, Rascu S, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Benhamou S, Cancel-Tassin G, Cussenot O, Weiderpass E, Ljungberg B, Tumkur Sitaram R, Häggström C, Bruinsma F, Jordan SJ, Severi G, Winship I, Hveem K, Vatten LJ, Fletcher T, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Andreotti G, Beane Freeman LE, Koutros S, Männistö S, Weinstein S, Clark PE, Edwards TL, Lipworth L, Gapstur SM, Stevens VL, Carol H, Freedman ML, Pomerantz MM, Cho E, Wilson KM, Gaziano JM, Sesso HD, Freedman ND, Parker AS, Eckel-Passow JE, Huang WY, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Teh BT, Peters U, White E, Anderson GL, Johnson L, Luo J, Buring J, Lee IM, Chow WH, Moore LE, Eisen T, Henrion M, Larkin J, Barman P, Leibovich BC, Choueiri TK, Lathrop GM, Deleuze JF, Gunter M, McKay JD, Wu X, Houlston RS, Chanock SJ, Relton C, Richards JB, Martin RM, Davey Smith G, Brennan P. The influence of obesity-related factors in the etiology of renal cell carcinoma-A mendelian randomization study. PLoS Med 2019; 16:e1002724. [PMID: 30605491 PMCID: PMC6317776 DOI: 10.1371/journal.pmed.1002724] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Several obesity-related factors have been associated with renal cell carcinoma (RCC), but it is unclear which individual factors directly influence risk. We addressed this question using genetic markers as proxies for putative risk factors and evaluated their relation to RCC risk in a mendelian randomization (MR) framework. This methodology limits bias due to confounding and is not affected by reverse causation. METHODS AND FINDINGS Genetic markers associated with obesity measures, blood pressure, lipids, type 2 diabetes, insulin, and glucose were initially identified as instrumental variables, and their association with RCC risk was subsequently evaluated in a genome-wide association study (GWAS) of 10,784 RCC patients and 20,406 control participants in a 2-sample MR framework. The effect on RCC risk was estimated by calculating odds ratios (ORSD) for a standard deviation (SD) increment in each risk factor. The MR analysis indicated that higher body mass index increases the risk of RCC (ORSD: 1.56, 95% confidence interval [CI] 1.44-1.70), with comparable results for waist-to-hip ratio (ORSD: 1.63, 95% CI 1.40-1.90) and body fat percentage (ORSD: 1.66, 95% CI 1.44-1.90). This analysis further indicated that higher fasting insulin (ORSD: 1.82, 95% CI 1.30-2.55) and diastolic blood pressure (DBP; ORSD: 1.28, 95% CI 1.11-1.47), but not systolic blood pressure (ORSD: 0.98, 95% CI 0.84-1.14), increase the risk for RCC. No association with RCC risk was seen for lipids, overall type 2 diabetes, or fasting glucose. CONCLUSIONS This study provides novel evidence for an etiological role of insulin in RCC, as well as confirmatory evidence that obesity and DBP influence RCC risk.
Collapse
Affiliation(s)
| | | | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Daniela Mariosa
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Nicolas J. Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Philip C. Haycock
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Zhaoming Wang
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jonathan N. Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Leandro M. Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Peng Li
- International Agency for Research on Cancer (IARC), Lyon, France
- Max Planck Institute for Demographic Research, Rostock, Germany
| | - Jean-Guillaume Garnier
- Centre National de Genotypage, Institut de Genomique, Centre de l'Energie Atomique et aux Energies Alternatives, Evry, France
- Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Helene Blanche
- Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Anne Boland
- Centre National de Genotypage, Institut de Genomique, Centre de l'Energie Atomique et aux Energies Alternatives, Evry, France
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Egor Prokhortchouk
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin G. Skryabin
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russian Federation
- Kurchatov Scientific Center, Moscow, Russian Federation
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Sanja Radojevic-Skodric
- Institute of Pathology, Medical School of Belgrade, Belgrade, Serbia
- Clinic of Urology, Clinical Center of Serbia, Belgrade, Serbia
| | - Simona Ognjanovic
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, United States of America
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Stefan Rascu
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Bencko
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Eleonora Fabianova
- Regional Authority of Public Health in Banska Bystrica, Banska Bystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Center, National Directorate of Environmental Health, Budapest, Hungary
| | - Simone Benhamou
- INSERM U946, Paris, France
- CNRS UMR8200, Institute Gustave Roussy, Villejuif, France
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France
- UPMC Univ Paris 06, GRC n°5, Institut Universitaire de Cancérologie, Paris, France
| | - Olivier Cussenot
- CeRePP, Paris, France
- UPMC Univ Paris 06, GRC n°5, Institut Universitaire de Cancérologie, Paris, France
- AP-HP, Department of Urology, Hopitaux Universitaires Est Parisien Tenon, Paris, France
| | - Elisabete Weiderpass
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Genetic Epidemiology Group, Folkhälsan Research Center, Helsinki, Finland
- Department of Community Medicine, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | | | - Christel Häggström
- Department of Biobank Research, Umeå University, Umeå, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Susan J. Jordan
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Public Health, The University of Queensland, Brisbane, Australia
| | - Gianluca Severi
- “Health across generations” team, CESP Inserm, Facultés de Médicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Ingrid Winship
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Kristian Hveem
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars J. Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
| | - Susanna C. Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E. Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Peter J. Selby
- National Institute for Health Research Diagnostic Evidence Cooperative, Division of Surgery, Imperial College London, St Mary’s Hospital, London, United Kingdom
| | - Douglas F. Easton
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Peter E. Clark
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - Todd L. Edwards
- Department of Medicine, Division of Epidemiology, Vanderbilt-Ingram Cancer Center, Vanderbilt Genetics Institute, Nashville, Tennessee, United States of America
| | - Loren Lipworth
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - Susan M. Gapstur
- American Cancer Society, Atlanta, Georgia, United States of America
| | | | - Hallie Carol
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Mark M. Pomerantz
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Eunyoung Cho
- Brown University, Providence, Rhode Island, United States of America
| | - Kathryn M. Wilson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - J. Michael Gaziano
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Howard D. Sesso
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Alexander S. Parker
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Jeanette E. Eckel-Passow
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Richard J. Kahnoski
- Division of Urology, Spectrum Health, Grand Rapids, Michigan, United States of America
| | - Brian R. Lane
- Division of Urology, Spectrum Health, Grand Rapids, Michigan, United States of America
- College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
| | - Sabrina L. Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan, United States of America
- Spectrum Health, Grand Rapids, Michigan, United States of America
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan, United States of America
- Diagnostics Program at Ferris State University, Grand Rapids, Michigan, United States of America
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan, United States of America
- Program in Cancer and Stem Cell Biology, Duke-National, University of Singapore Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ulrike Peters
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Garnet L. Anderson
- WHI Clinical Coordinating Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lisa Johnson
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, Indiana, United States of America
| | - Julie Buring
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - I-Min Lee
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lee E. Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | | | - Marc Henrion
- The Institute of Cancer Research, London, United Kingdom
- Dept. of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - James Larkin
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Poulami Barman
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Bradley C. Leibovich
- Department of Urology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Toni K. Choueiri
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - G. Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jean-Francois Deleuze
- Centre National de Genotypage, Institut de Genomique, Centre de l'Energie Atomique et aux Energies Alternatives, Evry, France
- Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Marc Gunter
- International Agency for Research on Cancer (IARC), Lyon, France
| | - James D. McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - J. Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Richard M. Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust National Institute for Health Research Bristol Nutrition Biomedical Research Unit, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| |
Collapse
|
10
|
Affiliation(s)
- Joseph M Lewis
- Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| | - Marc Henrion
- Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| | - Jamie Rylance
- Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| |
Collapse
|
11
|
Machiela MJ, Hofmann JN, Carreras-Torres R, Brown KM, Johansson M, Wang Z, Foll M, Li P, Rothman N, Savage SA, Gaborieau V, McKay JD, Ye Y, Henrion M, Bruinsma F, Jordan S, Severi G, Hveem K, Vatten LJ, Fletcher T, Koppova K, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Pharoah P, Andreotti G, Freeman LEB, Koutros S, Albanes D, Mannisto S, Weinstein S, Clark PE, Edwards TE, Lipworth L, Gapstur SM, Stevens VL, Carol H, Freedman ML, Pomerantz MM, Cho E, Kraft P, Preston MA, Wilson KM, Gaziano JM, Sesso HS, Black A, Freedman ND, Huang WY, Anema JG, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Colli LM, Sampson JN, Besse C, Blanche H, Boland A, Burdette L, Prokhortchouk E, Skryabin KG, Yeager M, Mijuskovic M, Ognjanovic M, Foretova L, Holcatova I, Janout V, Mates D, Mukeriya A, Rascu S, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Szeszenia-Dabrowska N, Benhamou S, Cancel-Tassin G, Cussenot O, Bueno-de-Mesquita HBA, Canzian F, Duell EJ, Ljungberg B, Sitaram RT, Peters U, White E, Anderson GL, Johnson L, Luo J, Buring J, Lee IM, Chow WH, Moore LE, Wood C, Eisen T, Larkin J, Choueiri TK, Lathrop GM, Teh BT, Deleuze JF, Wu X, Houlston RS, Brennan P, Chanock SJ, Scelo G, Purdue MP. Corrigendum re "Genetic Variants Related to Longer Telomere Length are Associated with Increased Risk of Renal Cell Carcinoma" [Eur Urol 2017;72:747-54]. Eur Urol 2018; 74:e85-e86. [PMID: 29853305 PMCID: PMC7400767 DOI: 10.1016/j.eururo.2018.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Zhaoming Wang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Peng Li
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - James D McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Fiona Bruinsma
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
| | - Susan Jordan
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; School of Public Health, The University of Queensland, Brisbane, Australia
| | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Australia; Human Genetics Foundation (HuGeF), Torino, Italy; Centre de Recherche en Épidémiologie et Santé des Populations, Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Sweden
| | - Lars J Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Kvetoslava Koppova
- Regional Authority of Public Health in Banska Bystrica, Banska Bystrica, Slovakia
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Douglas F Easton
- Department of Oncology, and Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Oncology, and Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Satu Mannisto
- National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | | | | | | | | | | | | | | | | | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - J Michael Gaziano
- Brigham and Women's Hospital, Boston, MA, USA; Veterans Administration, Boston, MA, USA
| | - Howard S Sesso
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - John G Anema
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
| | | | - Brian R Lane
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA; College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Sabrina L Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Celine Besse
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
| | - Helene Blanche
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Anne Boland
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Egor Prokhortchouk
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation; Kurchatov Scientific Center, Moscow, Russian Federation
| | - Konstantin G Skryabin
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation; Kurchatov Scientific Center, Moscow, Russian Federation
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Miodrag Ognjanovic
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Second Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Stefan Rascu
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Bencko
- First Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University, Prague, Czech Republic
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Eleonora Fabianova
- Regional Authority of Public Health in Banska Bystrica, Banska Bystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Center, National Directorate of Environmental Health, Budapest, Hungary
| | | | - Simone Benhamou
- INSERM U946, Paris, France; CNRS UMR8200, Institute Gustave Roussy, Villejuif, France
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France; UPMC Univ Paris 06, Institut Universitaire de Cancérologie, Paris, France
| | - Olivier Cussenot
- CeRePP, Paris, France; UPMC Univ Paris 06, Institut Universitaire de Cancérologie, Paris, France; AP-HP, Department of Urology, Hopitaux Universitaires Est Parisien Tenon, Paris, France
| | - H B As Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands; Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, UK; Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Pantai Valley, Kuala Lumpur, Malaysia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Raviprakash T Sitaram
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lisa Johnson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, IN, USA
| | - Julie Buring
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - I-Min Lee
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Christopher Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - G Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Jean-Francois Deleuze
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France; Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA.
| |
Collapse
|
12
|
Shwe MA, Heckerman DE, Henrion M, Horvitz EJ, Lehmann HP, Cooper GF, Middleton B. Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base. Methods Inf Med 2018. [DOI: 10.1055/s-0038-1634846] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract:In Part I of this two-part series, we report the design of a probabilistic reformulation of the Quick Medical Reference (QMR) diagnostic decision-support tool. We describe a two-level multiply connected belief-network representation of the QMR knowledge base of internal medicine. In the belief-network representation of the QMR knowledge base, we use probabilities derived from the QMR disease profiles, from QMR imports of findings, and from National Center for Health Statistics hospital-discharge statistics.We use a stochastic simulation algorithm for inference on the belief network. This algorithm computes estimates of the posterior marginal probabilities of diseases given a set of findings. In Part II of the series, we compare the performance of QMR to that of our probabilistic system on cases abstracted from continuing medical education materials from Scientific American Medicine. In addition, we analyze empirically several components of the probabilistic model and simulation algorithm.
Collapse
|
13
|
Shwe AM, Heckerman ED, Henrion M, Horvitz JE, Lehmann PH, Cooper FG, Middleton B. Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base. Methods Inf Med 2018. [DOI: 10.1055/s-0038-1634847] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractWe have developed a probabilistic reformulation of the Quick Medical Reference (QMR) system. In Part I of this two-part series, we described a two-level, multiply connected belief-network representation of the QMR knowledge base and a simulation algorithm to perform probabilistic inference on the reformulated knowledge base. In Part II of this series, we report on an evaluation of the probabilistic QMR, in which we compare the performance of QMR to that of our probabilistic system on cases abstracted from continuing medical education materials from Scientific American Medicine. In addition, we analyze empirically several components of the probabilistic model and simulation algorithm.
Collapse
|
14
|
Machiela MJ, Hofmann JN, Carreras-Torres R, Brown KM, Johansson M, Wang Z, Foll M, Li P, Rothman N, Savage SA, Gaborieau V, McKay JD, Ye Y, Henrion M, Bruinsma F, Jordan S, Severi G, Hveem K, Vatten LJ, Fletcher T, Koppova K, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Pharoah P, Andreotti G, Freeman LEB, Koutros S, Albanes D, Mannisto S, Weinstein S, Clark PE, Edwards TE, Lipworth L, Gapstur SM, Stevens VL, Carol H, Freedman ML, Pomerantz MM, Cho E, Kraft P, Preston MA, Wilson KM, Gaziano JM, Sesso HS, Black A, Freedman ND, Huang WY, Anema JG, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Colli LM, Sampson JN, Besse C, Blanche H, Boland A, Burdette L, Prokhortchouk E, Skryabin KG, Yeager M, Mijuskovic M, Ognjanovic M, Foretova L, Holcatova I, Janout V, Mates D, Mukeriya A, Rascu S, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Szeszenia-Dabrowska N, Benhamou S, Cancel-Tassin G, Cussenot O, Bueno-de-Mesquita HB, Canzian F, Duell EJ, Ljungberg B, Sitaram RT, Peters U, White E, Anderson GL, Johnson L, Luo J, Buring J, Lee IM, Chow WH, Moore LE, Wood C, Eisen T, Larkin J, Choueiri TK, Lathrop GM, Teh BT, Deleuze JF, Wu X, Houlston RS, Brennan P, Chanock SJ, Scelo G, Purdue MP. Genetic Variants Related to Longer Telomere Length are Associated with Increased Risk of Renal Cell Carcinoma. Eur Urol 2017; 72:747-754. [PMID: 28797570 PMCID: PMC5641242 DOI: 10.1016/j.eururo.2017.07.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/17/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Relative telomere length in peripheral blood leukocytes has been evaluated as a potential biomarker for renal cell carcinoma (RCC) risk in several studies, with conflicting findings. OBJECTIVE We performed an analysis of genetic variants associated with leukocyte telomere length to assess the relationship between telomere length and RCC risk using Mendelian randomization, an approach unaffected by biases from temporal variability and reverse causation that might have affected earlier investigations. DESIGN, SETTING, AND PARTICIPANTS Genotypes from nine telomere length-associated variants for 10 784 cases and 20 406 cancer-free controls from six genome-wide association studies (GWAS) of RCC were aggregated into a weighted genetic risk score (GRS) predictive of leukocyte telomere length. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Odds ratios (ORs) relating the GRS and RCC risk were computed in individual GWAS datasets and combined by meta-analysis. RESULTS AND LIMITATIONS Longer genetically inferred telomere length was associated with an increased risk of RCC (OR=2.07 per predicted kilobase increase, 95% confidence interval [CI]:=1.70-2.53, p<0.0001). As a sensitivity analysis, we excluded two telomere length variants in linkage disequilibrium (R2>0.5) with GWAS-identified RCC risk variants (rs10936599 and rs9420907) from the telomere length GRS; despite this exclusion, a statistically significant association between the GRS and RCC risk persisted (OR=1.73, 95% CI=1.36-2.21, p<0.0001). Exploratory analyses for individual histologic subtypes suggested comparable associations with the telomere length GRS for clear cell (N=5573, OR=1.93, 95% CI=1.50-2.49, p<0.0001), papillary (N=573, OR=1.96, 95% CI=1.01-3.81, p=0.046), and chromophobe RCC (N=203, OR=2.37, 95% CI=0.78-7.17, p=0.13). CONCLUSIONS Our investigation adds to the growing body of evidence indicating some aspect of longer telomere length is important for RCC risk. PATIENT SUMMARY Telomeres are segments of DNA at chromosome ends that maintain chromosomal stability. Our study investigated the relationship between genetic variants associated with telomere length and renal cell carcinoma risk. We found evidence suggesting individuals with inherited predisposition to longer telomere length are at increased risk of developing renal cell carcinoma.
Collapse
Affiliation(s)
- Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Zhaoming Wang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Peng Li
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - James D McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Fiona Bruinsma
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
| | - Susan Jordan
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; School of Public Health, The University of Queensland, Brisbane, Australia
| | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Australia; Human Genetics Foundation (HuGeF), Torino, Italy; Centre de Recherche en Épidémiologie et Santé des Populations, Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Sweden
| | - Lars J Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Kvetoslava Koppova
- Regional Authority of Public Health in Banska Bystrica, Banska Bystrica, Slovakia
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Douglas F Easton
- Department of Oncology, and Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Oncology, and Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Satu Mannisto
- National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | | | | | | | | | | | | | | | | | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - J Michael Gaziano
- Brigham and Women's Hospital, Boston, MA, USA; Veterans Administration, Boston, MA, USA
| | - Howard S Sesso
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - John G Anema
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
| | | | - Brian R Lane
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA; College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Sabrina L Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Celine Besse
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
| | - Helene Blanche
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Anne Boland
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Egor Prokhortchouk
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation; Kurchatov Scientific Center, Moscow, Russian Federation
| | - Konstantin G Skryabin
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation; Kurchatov Scientific Center, Moscow, Russian Federation
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | | | - Miodrag Ognjanovic
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | - Lenka Foretova
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | - Ivana Holcatova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Janout
- Second Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, Prague, Czech Republic
| | - Dana Mates
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Czech Republic
| | | | - Stefan Rascu
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - David Zaridze
- National Institute of Public Health, Bucharest, Romania
| | - Vladimir Bencko
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Cezary Cybulski
- First Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University, Prague, Czech Republic
| | - Eleonora Fabianova
- Regional Authority of Public Health in Banska Bystrica, Banska Bystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Center, National Directorate of Environmental Health, Budapest, Hungary
| | | | - Simone Benhamou
- INSERM U946, Paris, France; CNRS UMR8200, Institute Gustave Roussy, Villejuif, France
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France; UPMC Univ Paris 06, Institut Universitaire de Cancérologie, Paris, France
| | - Olivier Cussenot
- CeRePP, Paris, France; UPMC Univ Paris 06, Institut Universitaire de Cancérologie, Paris, France; AP-HP, Department of Urology, Hopitaux Universitaires Est Parisien Tenon, Paris, France
| | - H Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands; Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, UK; Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Pantai Valley, Kuala Lumpur, Malaysia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Raviprakash T Sitaram
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lisa Johnson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, IN, USA
| | - Julie Buring
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - I-Min Lee
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Christopher Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - G Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Jean-Francois Deleuze
- Centre National de Recherche en Genomique Humaine (CNRGH), Institut de biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France; Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MS, USA.
| |
Collapse
|
15
|
Went M, Sud A, Law PJ, Johnson DC, Weinhold N, Försti A, van Duin M, Mitchell JS, Chen B, Kuiper R, Stephens OW, Bertsch U, Campo C, Einsele H, Gregory WM, Henrion M, Hillengass J, Hoffmann P, Jackson GH, Lenive O, Nickel J, Nöthen MM, da Silva Filho MI, Thomsen H, Walker BA, Broyl A, Davies FE, Langer C, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Hemminki K, Nilsson B, Morgan GJ, Houlston RS. Assessing the effect of obesity-related traits on multiple myeloma using a Mendelian randomisation approach. Blood Cancer J 2017; 7. [PMID: 28622301 PMCID: PMC5520395 DOI: 10.1038/bcj.2017.48] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- M Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - A Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - P J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - D C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - N Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - A Försti
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmo, Sweden
| | - M van Duin
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - J S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - B Chen
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - R Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - O W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - U Bertsch
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - C Campo
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - H Einsele
- Department of Internal Medicine II, Division of Hematology and Medical Oncology, University Hospital Würzburg, Würzburg, Germany
| | - W M Gregory
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - M Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - J Hillengass
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - G H Jackson
- Royal Victoria Infirmary, Newcastle upon Tyne, Newcastle, UK
| | - O Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - J Nickel
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - M I da Silva Filho
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - H Thomsen
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - B A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Broyl
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - F E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Langer
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - M Hansson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Hematology Clinic, Skåne University Hospital, Lund, Sweden
| | - M Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - P Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - H Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - K Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmo, Sweden
| | - B Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - G J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- E-mail:
| |
Collapse
|
16
|
Scelo G, Purdue MP, Brown KM, Johansson M, Wang Z, Eckel-Passow JE, Ye Y, Hofmann JN, Choi J, Foll M, Gaborieau V, Machiela MJ, Colli LM, Li P, Sampson JN, Abedi-Ardekani B, Besse C, Blanche H, Boland A, Burdette L, Chabrier A, Durand G, Le Calvez-Kelm F, Prokhortchouk E, Robinot N, Skryabin KG, Wozniak MB, Yeager M, Basta-Jovanovic G, Dzamic Z, Foretova L, Holcatova I, Janout V, Mates D, Mukeriya A, Rascu S, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Szeszenia-Dabrowska N, Benhamou S, Cancel-Tassin G, Cussenot O, Baglietto L, Boeing H, Khaw KT, Weiderpass E, Ljungberg B, Sitaram RT, Bruinsma F, Jordan SJ, Severi G, Winship I, Hveem K, Vatten LJ, Fletcher T, Koppova K, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Pharoah P, Andreotti G, Freeman LEB, Koutros S, Albanes D, Männistö S, Weinstein S, Clark PE, Edwards TL, Lipworth L, Gapstur SM, Stevens VL, Carol H, Freedman ML, Pomerantz MM, Cho E, Kraft P, Preston MA, Wilson KM, Michael Gaziano J, Sesso HD, Black A, Freedman ND, Huang WY, Anema JG, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Teh BT, Peters U, White E, Anderson GL, Johnson L, Luo J, Buring J, Lee IM, Chow WH, Moore LE, Wood C, Eisen T, Henrion M, Larkin J, Barman P, Leibovich BC, Choueiri TK, Mark Lathrop G, Rothman N, Deleuze JF, McKay JD, Parker AS, Wu X, Houlston RS, Brennan P, Chanock SJ. Genome-wide association study identifies multiple risk loci for renal cell carcinoma. Nat Commun 2017; 8:15724. [PMID: 28598434 PMCID: PMC5472706 DOI: 10.1038/ncomms15724] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/24/2017] [Indexed: 12/21/2022] Open
Abstract
Previous genome-wide association studies (GWAS) have identified six risk loci for renal cell carcinoma (RCC). We conducted a meta-analysis of two new scans of 5,198 cases and 7,331 controls together with four existing scans, totalling 10,784 cases and 20,406 controls of European ancestry. Twenty-four loci were tested in an additional 3,182 cases and 6,301 controls. We confirm the six known RCC risk loci and identify seven new loci at 1p32.3 (rs4381241, P=3.1 × 10-10), 3p22.1 (rs67311347, P=2.5 × 10-8), 3q26.2 (rs10936602, P=8.8 × 10-9), 8p21.3 (rs2241261, P=5.8 × 10-9), 10q24.33-q25.1 (rs11813268, P=3.9 × 10-8), 11q22.3 (rs74911261, P=2.1 × 10-10) and 14q24.2 (rs4903064, P=2.2 × 10-24). Expression quantitative trait analyses suggest plausible candidate genes at these regions that may contribute to RCC susceptibility.
Collapse
Affiliation(s)
- Ghislaine Scelo
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zhaoming Wang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Jonathan N. Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Valerie Gaborieau
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Leandro M. Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Peng Li
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | | | - Celine Besse
- Centre National de Genotypage, Institut de Genomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, 91057 Evry, France
| | - Helene Blanche
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Anne Boland
- Centre National de Genotypage, Institut de Genomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, 91057 Evry, France
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Amelie Chabrier
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Egor Prokhortchouk
- Center ‘Bioengineering' of the Russian Academy of Sciences, Moscow 117312, Russia
- Kurchatov Scientific Center, Moscow 123182, Russia
| | | | - Konstantin G. Skryabin
- Center ‘Bioengineering' of the Russian Academy of Sciences, Moscow 117312, Russia
- Kurchatov Scientific Center, Moscow 123182, Russia
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | | | - Zoran Dzamic
- Clinical Center of Serbia (KCS), Clinic of Urology, University of Belgrade-Faculty of Medicine, 11000 Belgrade, Serbia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, 150 06 Prague 5, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, 775 15 Olomouc, Czech Republic
| | - Dana Mates
- National Institute of Public Health, 050463 Bucharest, Romania
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Stefan Rascu
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, 050659 Bucharest, Romania
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Vladimir Bencko
- First Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University, 128 00 Prague 2, Czech Republic
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Eleonora Fabianova
- Regional Authority of Public Health in Banska Bystrica, 975 56 Banska Bystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, 050659 Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, 02-034 Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Center, National Directorate of Environmental Health, 1097 Budapest, Hungary
| | | | - Simone Benhamou
- Université Paris Diderot, INSERM, Unité Variabilité Génétique et Maladies Humaines, 75010 Paris, France
| | | | - Olivier Cussenot
- CeRePP, Tenon Hospital, 75020 Paris, France
- UPMC Univ Paris 06 GRC n°5, 75013 Paris, France
| | - Laura Baglietto
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, 94805 Villejuif, France
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, 14558 Nuthetal, Germany
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, 0304 Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Genetic Epidemiology Group, Folkhälsan Research Center, 00250 Helsinki, Finland
| | - Borje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, 901 85 Umeå, Sweden
| | - Raviprakash T. Sitaram
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, 901 85 Umeå, Sweden
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - Susan J. Jordan
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
- School of Public Health, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, 94805 Villejuif, France
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria 3053, Australia
- Human Genetics Foundation (HuGeF), 10126 Torino, Italy
| | - Ingrid Winship
- Department of Medicine, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger 7600, Norway
| | - Lars J. Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London WC1H 9SH, UK
| | - Kvetoslava Koppova
- Regional Authority of Public Health in Banska Bystrica, 975 56 Banska Bystrica, Slovakia
| | - Susanna C. Larsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rosamonde E. Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds LS9 7TF, UK
| | - Peter J. Selby
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds LS9 7TF, UK
| | - Douglas F. Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Peter E. Clark
- Vanderbilt-Ingram Cancer Center, Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Todd L. Edwards
- Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37209, USA
| | - Loren Lipworth
- Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | | | | | - Hallie Carol
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | | | | | - Eunyoung Cho
- Warren Alpert Medical School of Brown University, Providence, Rhode Island 02903, USA
| | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Mark A. Preston
- Brigham and Women's Hospital and VA Boston, Boston, Massachusetts 02115, USA
| | - Kathryn M. Wilson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - J. Michael Gaziano
- Brigham and Women's Hospital and VA Boston, Boston, Massachusetts 02115, USA
| | - Howard D. Sesso
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Brigham and Women's Hospital and VA Boston, Boston, Massachusetts 02115, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - John G. Anema
- Division of Urology, Spectrum Health, Grand Rapids, Michigan 49503, USA
| | | | - Brian R. Lane
- Division of Urology, Spectrum Health, Grand Rapids, Michigan 49503, USA
- College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Sabrina L. Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan 49503, USA
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan 49503, USA
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, Michigan 49503, USA
| | - Ulrike Peters
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Garnet L. Anderson
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Lisa Johnson
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, Indiana 47405, USA
| | - Julie Buring
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Brigham and Women's Hospital and VA Boston, Boston, Massachusetts 02115, USA
| | - I-Min Lee
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Brigham and Women's Hospital and VA Boston, Boston, Massachusetts 02115, USA
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Lee E. Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Christopher Wood
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Marc Henrion
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - James Larkin
- Medical Oncology, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Poulami Barman
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Bradley C. Leibovich
- Department of Urology, Mayo Medical School and Mayo Clinic, Rochester, Minnesota 55902, USA
| | | | - G. Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada H3A 0G1
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| | - Jean-Francois Deleuze
- Centre National de Genotypage, Institut de Genomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, 91057 Evry, France
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - James D. McKay
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexander S. Parker
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida 32224, USA
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland 20892, USA
| |
Collapse
|
17
|
Law PJ, Sud A, Mitchell JS, Henrion M, Orlando G, Lenive O, Broderick P, Speedy HE, Johnson DC, Kaiser M, Weinhold N, Cooke R, Sunter NJ, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Carmichael J, Bailey JR, Pratt G, Rahman T, Pepper C, Fegan C, von Strandmann EP, Engert A, Försti A, Chen B, Filho MIDS, Thomsen H, Hoffmann P, Noethen MM, Eisele L, Jöckel KH, Allan JM, Swerdlow AJ, Goldschmidt H, Catovsky D, Morgan GJ, Hemminki K, Houlston RS. Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. Sci Rep 2017; 7:41071. [PMID: 28112199 PMCID: PMC5253627 DOI: 10.1038/srep41071] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/14/2016] [Indexed: 02/08/2023] Open
Abstract
B-cell malignancies (BCM) originate from the same cell of origin, but at different maturation stages and have distinct clinical phenotypes. Although genetic risk variants for individual BCMs have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. We explored genome-wide association studies of chronic lymphocytic leukaemia (CLL, N = 1,842), Hodgkin lymphoma (HL, N = 1,465) and multiple myeloma (MM, N = 3,790). We identified a novel pleiotropic risk locus at 3q22.2 (NCK1, rs11715604, P = 1.60 × 10-9) with opposing effects between CLL (P = 1.97 × 10-8) and HL (P = 3.31 × 10-3). Eight established non-HLA risk loci showed pleiotropic associations. Within the HLA region, Ser37 + Phe37 in HLA-DRB1 (P = 1.84 × 10-12) was associated with increased CLL and HL risk (P = 4.68 × 10-12), and reduced MM risk (P = 1.12 × 10-2), and Gly70 in HLA-DQB1 (P = 3.15 × 10-10) showed opposing effects between CLL (P = 3.52 × 10-3) and HL (P = 3.41 × 10-9). By integrating eQTL, Hi-C and ChIP-seq data, we show that the pleiotropic risk loci are enriched for B-cell regulatory elements, as well as an over-representation of binding of key B-cell transcription factors. These data identify shared biological pathways influencing the development of CLL, HL and MM. The identification of these risk loci furthers our understanding of the aetiological basis of BCMs.
Collapse
Affiliation(s)
- Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nicola J. Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Graham H. Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Geoffrey Summerfield
- Department of Haematology, Queen Elizabeth Hospital, Gateshead, Newcastle upon Tyne, UK
| | - Robert J. Harris
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - David J. Allsup
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Jonathan Carmichael
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - James R. Bailey
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Thahira Rahman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | | | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland
| | - Markus M. Noethen
- Institute of Human Genetics, University of Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Germany
| | | | | | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center of Tumor Diseases, Heidelberg, Germany
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| |
Collapse
|
18
|
Mitchell JS, Li N, Weinhold N, Försti A, Ali M, van Duin M, Thorleifsson G, Johnson DC, Chen B, Halvarsson BM, Gudbjartsson DF, Kuiper R, Stephens OW, Bertsch U, Broderick P, Campo C, Einsele H, Gregory WA, Gullberg U, Henrion M, Hillengass J, Hoffmann P, Jackson GH, Johnsson E, Jöud M, Kristinsson SY, Lenhoff S, Lenive O, Mellqvist UH, Migliorini G, Nahi H, Nelander S, Nickel J, Nöthen MM, Rafnar T, Ross FM, da Silva Filho MI, Swaminathan B, Thomsen H, Turesson I, Vangsted A, Vogel U, Waage A, Walker BA, Wihlborg AK, Broyl A, Davies FE, Thorsteinsdottir U, Langer C, Hansson M, Kaiser M, Sonneveld P, Stefansson K, Morgan GJ, Goldschmidt H, Hemminki K, Nilsson B, Houlston RS. Genome-wide association study identifies multiple susceptibility loci for multiple myeloma. Nat Commun 2016; 7:12050. [PMID: 27363682 PMCID: PMC4932178 DOI: 10.1038/ncomms12050] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/24/2016] [Indexed: 02/08/2023] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy with a significant heritable basis. Genome-wide association studies have transformed our understanding of MM predisposition, but individual studies have had limited power to discover risk loci. Here we perform a meta-analysis of these GWAS, add a new GWAS and perform replication analyses resulting in 9,866 cases and 239,188 controls. We confirm all nine known risk loci and discover eight new loci at 6p22.3 (rs34229995, P=1.31 × 10(-8)), 6q21 (rs9372120, P=9.09 × 10(-15)), 7q36.1 (rs7781265, P=9.71 × 10(-9)), 8q24.21 (rs1948915, P=4.20 × 10(-11)), 9p21.3 (rs2811710, P=1.72 × 10(-13)), 10p12.1 (rs2790457, P=1.77 × 10(-8)), 16q23.1 (rs7193541, P=5.00 × 10(-12)) and 20q13.13 (rs6066835, P=1.36 × 10(-13)), which localize in or near to JARID2, ATG5, SMARCD3, CCAT1, CDKN2A, WAC, RFWD3 and PREX1. These findings provide additional support for a polygenic model of MM and insight into the biological basis of tumour development.
Collapse
Affiliation(s)
- Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Asta Försti
- German Cancer Research Center, 69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02 Malmo, Sweden
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | | | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, Surrey SM2 5NG, UK
| | - Bowang Chen
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Daniel F. Gudbjartsson
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101 Reykjavik, Iceland
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | - Owen W. Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Uta Bertsch
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
- National Centre of Tumor Diseases, 69120 Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Chiara Campo
- German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Walter A. Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds LS2 9PH, UK
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | | | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Magnus Jöud
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, SE-221 85 Lund, Sweden
| | - Sigurður Y. Kristinsson
- Department of Hematology, Landspitali, National University Hospital of Iceland, IS-101 Reykjavik, Iceland
| | - Stig Lenhoff
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Sven Nelander
- Rudbeck Laboratory, Department of Immunology, Pathology and Genetics, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127 Bonn, Germany
| | - Thorunn Rafnar
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Fiona M. Ross
- Wessex Regional Genetics Laboratory, University of Southampton, Salisbury SP2 8BJ, UK
| | | | - Bhairavi Swaminathan
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Hauke Thomsen
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, DK-2100 Copenhagen, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491 Trondheim, Norway
| | - Brian A. Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | - Faith E. Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Christian Langer
- Department of Internal Medicine III, University of Ulm, D-89081 Ulm, Germany
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, Surrey SM2 5NG, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | | | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
- National Centre of Tumor Diseases, 69120 Heidelberg, Germany
| | - Kari Hemminki
- German Cancer Research Center, 69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02 Malmo, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, SE-221 85 Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| |
Collapse
|
19
|
Vijayakrishnan J, Henrion M, Moorman AV, Fiege B, Kumar R, Inacio da Silva Filho M, Holroyd A, Koehler R, Thomsen H, Irving JA, Allan JM, Lightfoot T, Roman E, Kinsey SE, Sheridan E, Thompson PD, Hoffmann P, Nöthen MM, Mühleisen TW, Eisele L, Bartram CR, Schrappe M, Greaves M, Hemminki K, Harrison CJ, Stanulla M, Houlston RS. The 9p21.3 risk of childhood acute lymphoblastic leukaemia is explained by a rare high-impact variant in CDKN2A. Sci Rep 2015; 5:15065. [PMID: 26463672 PMCID: PMC4604478 DOI: 10.1038/srep15065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/12/2015] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have provided strong evidence for inherited predisposition to childhood acute lymphoblastic leukaemia (ALL) identifying a number of risk loci. We have previously shown common SNPs at 9p21.3 influence ALL risk. These SNP associations are generally not themselves candidates for causality, but simply act as markers for functional variants. By means of imputation of GWAS data and subsequent validation SNP genotyping totalling 2,177 ALL cases and 8,240 controls, we have shown that the 9p21.3 association can be ascribed to the rare high-impact CDKN2A p.Ala148Thr variant (rs3731249; Odds ratio = 2.42, P = 3.45 × 10(-19)). The association between rs3731249 genotype and risk was not specific to particular subtype of B-cell ALL. The rs3731249 variant is associated with predominant nuclear localisation of the CDKN2A transcript suggesting the functional effect of p.Ala148Thr on ALL risk may be through compromised ability to inhibit cyclin D within the cytoplasm.
Collapse
Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Anthony V. Moorman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bettina Fiege
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Rolf Koehler
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Julie A. Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tracy Lightfoot
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Sally E. Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, United Kingdom
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Eamonn Sheridan
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Pamela D. Thompson
- Paediatric and Familial Cancer, Institute of Cancer Sciences, Manchester, United Kingdom
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Genomic Imaging Group, Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany
| | | | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg–Essen, Essen, Germany
| | - Claus R. Bartram
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Martin Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mel Greaves
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Christine J. Harrison
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Stanulla
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| |
Collapse
|
20
|
Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, Whiffin N, Carnicer MJ, Broome L, Dryden N, Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O, Houlston RS. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 2015; 6:6178. [PMID: 25695508 PMCID: PMC4346635 DOI: 10.1038/ncomms7178] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/30/2014] [Indexed: 12/25/2022] Open
Abstract
Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.
Collapse
Affiliation(s)
- Roland Jäger
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Radhika Kandaswamy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Andreas Heindl
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Maria J. Carnicer
- Division of Molecular Pathology, Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Laura Broome
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Nicola Dryden
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Martin Enge
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| |
Collapse
|
21
|
Shi J, Chatterjee N, Rotunno M, Wang Y, Pesatori AC, Consonni D, Li P, Broderick P, Henrion M, Eisen T, Wang Z, Chen W, Dong Q, Albanes D, Thun M, Spitz M, Bertazzi PA, Caporaso N, Chanock S, Amos C, Houlston R, Landi MT. Abstract 2931: Inherited variation at chromosome 12p13.33 includingRAD52influences squamous cell lung carcinoma risk. Epidemiology 2014. [DOI: 10.1158/1538-7445.am2012-2931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
22
|
Jäger R, Migliorini G, Henrion M, Whiffin N, Broome L, Dryden N, Nagano T, Schoenfelder S, Fraser P, Fletcher O, Houlston R. Abstract 407: Targeted Hi-C and integrative analyses reveal functionality of colorectal cancer risk loci. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genetic risk factors identified by genome-wide association studies (GWAS) are thought to function through allele-specific regulation of gene expression. Long-range chromatin looping interactions, as revealed by chromosome conformation capture (3C)-based techniques, bring risk variants into spatial proximity with loci otherwise distal on the linear genome. Hi-C, using next generation sequencing (NGS), allows for genome-wide agnostic characterization of chromatin contacts, however, detection of functional enhancer-promoter interactions is precluded by its limited resolution. Here we apply Targeted Hi-C, a novel technique combining the unbiased coverage of Hi-C with target sequence capture to identify functional chromatin interactions for 15 colorectal cancer risk loci at high resolution. We depicted the CRC risk interactome as a set of generic highly significant genome-wide interactions, predominantly overlaying the strongest risk association signals. Integrative analyses involving profiles for epigenetic marks, evolutionary conservation and transcription factor binding, revealed regulatory function of long-range chromatin interactions. At the 8q24.21 risk locus, we could extend a previously reported contact between rs6983267 and the MYC promoter to a network of interactions involving CCAT1 (colorectal cancer associated transcript 1). At other risk loci, our data supports the central role of TERC, BMP4, GREM1, BMP2, SMAD7 and in CRC pathogenesis. Additionally, distal to the risk loci we identified contacts with the genes such as TRPS1, TPO, ETS1, VEZT and RAN, previously implicated in cancer and mutated in CRC. Our results demonstrate the capability of high resolution chromatin interaction analyses in conjunction with combinatorial integrative analyses to decipher disease risk loci.
Citation Format: Roland Jäger, Gabriele Migliorini, Marc Henrion, Nicola Whiffin, Laura Broome, Nicola Dryden, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Olivia Fletcher, Richard Houlston. Targeted Hi-C and integrative analyses reveal functionality of colorectal cancer risk loci. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 407. doi:10.1158/1538-7445.AM2014-407
Collapse
Affiliation(s)
- Roland Jäger
- 1Institute of Cancer Research, Sutton, United Kingdom
| | | | - Marc Henrion
- 1Institute of Cancer Research, Sutton, United Kingdom
| | | | - Laura Broome
- 2Institute of Cancer Research, London, United Kingdom
| | - Nicola Dryden
- 2Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | | |
Collapse
|
23
|
Wang Y, McKay JD, Rafnar T, Wang Z, Timofeeva M, Broderick P, Zong X, Laplana M, Wei Y, Han Y, Lloyd A, Delahaye-Sourdeix M, Chubb D, Gaborieau V, Wheeler W, Chatterjee N, Thorleifsson G, Sulem P, Liu G, Kaaks R, Henrion M, Kinnersley B, Vallée M, LeCalvez-Kelm F, Stevens VL, Gapstur SM, Chen WV, Zaridze D, Szeszenia-Dabrowska N, Lissowska J, Rudnai P, Fabianova E, Mates D, Bencko V, Foretova L, Janout V, Krokan HE, Gabrielsen ME, Skorpen F, Vatten L, Njølstad I, Chen C, Goodman G, Benhamou S, Vooder T, Valk K, Nelis M, Metspalu A, Lener M, Lubiński J, Johansson M, Vineis P, Agudo A, Clavel-Chapelon F, Bueno-de-Mesquita H, Trichopoulos D, Khaw KT, Johansson M, Weiderpass E, Tjønneland A, Riboli E, Lathrop M, Scelo G, Albanes D, Caporaso NE, Ye Y, Gu J, Wu X, Spitz MR, Dienemann H, Rosenberger A, Su L, Matakidou A, Eisen T, Stefansson K, Risch A, Chanock SJ, Christiani DC, Hung RJ, Brennan P, Landi MT, Houlston RS, Amos CI. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat Genet 2014; 46:736-41. [PMID: 24880342 PMCID: PMC4074058 DOI: 10.1038/ng.3002] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 05/08/2014] [Indexed: 12/16/2022]
Abstract
We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.
Collapse
Affiliation(s)
- Yufei Wang
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - James D. McKay
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thorunn Rafnar
- deCODE genetics/Amgen, Sturlugata 8, 101 Reykjavik, Iceland
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Maria Timofeeva
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital. Toronto, Canada
| | - Marina Laplana
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yongyue Wei
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Younghun Han
- Center for Genomic Medicine Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 46 Centerra Parkway, Suite 330, Lebanon, NH 03766
| | - Amy Lloyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | | | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Valerie Gaborieau
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - William Wheeler
- Information Management Services, Inc., Rockville, MD 20852, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | | | - Patrick Sulem
- deCODE genetics/Amgen, Sturlugata 8, 101 Reykjavik, Iceland
| | - Geoffrey Liu
- Princess Margaret Hospital, University Health Network, Toronto, Canada
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc Henrion
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Maxime Vallée
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30301, USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30301, USA
| | - Wei V. Chen
- Department of Genetics, U.T. M.D. Anderson Cancer Center, Houston, TX 77030
| | - David Zaridze
- Institute of Carcinogenesis, Russian N.N. Blokhin Cancer Research Centre, 115478 Moscow, Russia
| | | | - Jolanta Lissowska
- The M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02781, Poland
| | - Peter Rudnai
- National Institute of Environmental Health, Budapest 1097, Hungary
| | - Eleonora Fabianova
- Regional Authority of Public Health, Banska’ Bystrica 97556, Slovak Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest 050463, Romania
| | - Vladimir Bencko
- 1st Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University in Prague, 12800 Prague 2, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic
| | | | - Hans E. Krokan
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Maiken Elvestad Gabrielsen
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Frank Skorpen
- Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine
| | - Lars Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Inger Njølstad
- Department of Community Medicine, University of Tromso, Tromso 9037, Norway
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gary Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Tonu Vooder
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristjan Valk
- Competence Centre on Reproductive Medicine and Biology, 50410 Tartu, Estonia
| | - Mari Nelis
- Estonian Genome Center, Institute of Molecular and Cell Biology, Tartu 51010, Estonia
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Andres Metspalu
- Estonian Genome Center, Institute of Molecular and Cell Biology, Tartu 51010, Estonia
| | - Marcin Lener
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- HuGeF Foundation, Torino, Italy
| | - Antonio Agudo
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Francoise Clavel-Chapelon
- INSERM, Centre for research in Epidemiology and Population Health (CESP), U1018, Nutrition, Hormones and Women’s Health team, F-94805, Villejuif, France
- Université Paris Sud, UMRS 1018, F-94805, Villejuif, France
- IGR, F-94805, Villejuif, France
| | - H.Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Bureau of Epidemiologic Research, Academy of Athens, 23 Alexandroupoleos Street, Athens, GR-115 27, Greece
- Hellenic Health Foundation, 13 Kaisareias Street, Athens, GR-115 27, Greece
| | - Kay-Tee Khaw
- University of Cambridge School of Clinical Medicine, Clinical Gerontology Unit Box 251, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå universitet, SE-901 87 Umeå, Sverige, Sweden
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Samfundet Folkhälsan, Helsinki, Finland
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Strandboulevarden 49, DK 2100 Copenhagen Ø, Denmark
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Mark Lathrop
- Centre d’Etude du Polymorphisme Humain (CEPH), Paris 75010, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Yuanqing Ye
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Gu
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xifeng Wu
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Margaret R. Spitz
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hendrik Dienemann
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Surgery, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University of Göttingen, Göttingen, Germany
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Athena Matakidou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Addenbrooke’s Hospital, Cambridge Biomedical Campus, Hill’s Road Cambridge CB2 0QQ, UK
| | | | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital. Toronto, Canada
| | - Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Christopher I. Amos
- Center for Genomic Medicine Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 46 Centerra Parkway, Suite 330, Lebanon, NH 03766
| |
Collapse
|
24
|
Henrion M, Frampton M, Scelo G, Purdue M, Ye Y, Broderick P, Ritchie A, Kaplan R, Meade A, McKay J, Johansson M, Lathrop M, Larkin J, Rothman N, Wang Z, Chow WH, Stevens VL, Diver WR, Gapstur SM, Albanes D, Virtamo J, Wu X, Brennan P, Chanock S, Eisen T, Houlston RS. Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer. Hum Mol Genet 2013. [DOI: 10.1093/hmg/ddt084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
25
|
Henrion M, Frampton M, Scelo G, Purdue M, Ye Y, Broderick P, Ritchie A, Kaplan R, Meade A, McKay J, Johansson M, Lathrop M, Larkin J, Rothman N, Wang Z, Chow WH, Stevens VL, Ryan Diver W, Gapstur SM, Albanes D, Virtamo J, Wu X, Brennan P, Chanock S, Eisen T, Houlston RS. Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer. Hum Mol Genet 2012. [PMID: 23184150 DOI: 10.1093/hmg/dds489] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genome-wide association studies (GWASs) of renal cell cancer (RCC) have identified four susceptibility loci thus far. To identify an additional RCC common susceptibility locus, we conducted a GWAS and performed a meta-analysis with published GWASs (totalling 2215 cases and 8566 controls of European background) and followed up the most significant association signals [nine single nucleotide polymorphisms (SNPs) in eight genomic regions] in 3739 cases and 8786 controls. A combined analysis identified a novel susceptibility locus mapping to 2q22.3 marked by rs12105918 (P = 1.80 × 10(-8); odds ratio 1.29, 95% CI: 1.18-1.41). The signal localizes to intron 2 of the ZEB2 gene (zinc finger E box-binding homeobox 2). Our findings suggest that genetic variation in ZEB2 influences the risk of RCC. This finding provides further insights into the genetic and biological basis of inherited genetic susceptibility to RCC.
Collapse
Affiliation(s)
- Marc Henrion
- Division of Genetics and Epidemiology, Section of Cancer Genetics, Institute of Cancer Research, Surrey SM2 5NG, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Henrion M, Hand DJ, Gandy A, Mortlock DJ. CASOS: a subspace method for anomaly detection in high dimensional astronomical databases. Stat Anal Data Min 2012. [DOI: 10.1002/sam.11167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
27
|
Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, Tenesa A, Spain S, Broderick P, Ooi LY, Domingo E, Smillie C, Henrion M, Frampton M, Martin L, Grimes G, Gorman M, Semple C, Ma Y, Barclay E, Prendergast J, Cazier JB, Olver B, Carvajal-Carmona LG, Ballereau S, Lloyd A, Vijayakrishnan J, Zgaga L, Rudan I, Theodoratou E, Starr JM, Deary I, Kirac I, Kovačević D, Aaltonen LA, Renkonen-Sinisalo L, Mecklin JP, Matsuda K, Nakamura Y, Okada Y, Gallinger S, Duggan DJ, Conti D, Newcomb P, Hopper J, Jenkins MA, Schumacher F, Casey G, Easton D, Shah M, Pharoah P, Lindblom A, Liu T, Smith CG, West H, Cheadle JP, Midgley R, Kerr DJ, Campbell H, Tomlinson IP, Houlston RS. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat Genet 2012; 44:770-6. [PMID: 22634755 PMCID: PMC4747430 DOI: 10.1038/ng.2293] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/30/2012] [Indexed: 12/12/2022]
Abstract
We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totaling 21,096 cases and 19,555 controls. We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 × 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 × 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 × 10(-10)) This brings the number of independent loci associated with CRC risk to 20 and provides further insight into the genetic architecture of inherited susceptibility to CRC.
Collapse
Affiliation(s)
- Malcolm G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Sara E Dobbins
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Susan Mary Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Angela M Jones
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Sarah Spain
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Li-Yin Ooi
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Enric Domingo
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Claire Smillie
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Matthew Frampton
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Graeme Grimes
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Colin Semple
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Yussanne Ma
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - James Prendergast
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | | | - Bianca Olver
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Stephane Ballereau
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Amy Lloyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Lina Zgaga
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | - Igor Rudan
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | | | | | - John M Starr
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8, 9AG
| | - Ian Deary
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8, 9AG
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, University Hospital Center ‘Sestre milosrdnice’, Zagreb, Croatia
| | - Dujo Kovačević
- Department of Surgery, University Hospital Center ‘Sestre milosrdnice’, Zagreb, Croatia
| | - Lauri A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | | | - Jukka-Pekka Mecklin
- Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - David J Duggan
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Polly Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Mark A. Jenkins
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Fredrick Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Douglas Easton
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Mitul Shah
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Paul Pharoah
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, S17176 Stockholm
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, S17176 Stockholm
| | | | - Christopher G Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Hannah West
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Jeremy P. Cheadle
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | | | - Rachel Midgley
- Department of Oncology, Oxford University, Radcliffe Infirmary, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - David J Kerr
- Department of Oncology, Oxford University, Radcliffe Infirmary, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - Harry Campbell
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| |
Collapse
|
28
|
Shi J, Chatterjee N, Rotunno M, Wang Y, Pesatori AC, Consonni D, Li P, Wheeler W, Broderick P, Henrion M, Eisen T, Wang Z, Chen W, Dong Q, Albanes D, Thun M, Spitz MR, Bertazzi PA, Caporaso NE, Chanock SJ, Amos CI, Houlston RS, Landi MT. Inherited variation at chromosome 12p13.33, including RAD52, influences the risk of squamous cell lung carcinoma. Cancer Discov 2011; 2:131-9. [PMID: 22585858 DOI: 10.1158/2159-8290.cd-11-0246] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UNLABELLED Although lung cancer is largely caused by tobacco smoking, inherited genetic factors play a role in its etiology. Genome-wide association studies in Europeans have only robustly demonstrated 3 polymorphic variations that influence the risk of lung cancer. Tumor heterogeneity may have hampered the detection of association signal when all lung cancer subtypes were analyzed together. In a genome-wide association study of 5,355 European ever-smoker lung cancer patients and 4,344 smoking control subjects, we conducted a pathway-based analysis in lung cancer histologic subtypes with 19,082 single-nucleotide polymorphisms mapping to 917 genes in the HuGE-defined "inflammation" pathway. We identified a susceptibility locus for squamous cell lung carcinoma at 12p13.33 (RAD52, rs6489769) and replicated the association in 3 independent studies totaling 3,359 squamous cell lung carcinoma cases and 9,100 controls (OR = 1.20, P(combined) = 2.3 × 10(-8)). SIGNIFICANCE The combination of pathway-based approaches and information on disease-specific subtypes can improve the identification of cancer susceptibility loci in heterogeneous diseases.
Collapse
Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Pradhan A, Henrion M, Provan G, del Favero B, Huang K. The sensitivity of belief networks to imprecise probabilities: an experimental investigation. ARTIF INTELL 1996. [DOI: 10.1016/0004-3702(96)81368-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Small MJ, Cosby BJ, Marnicio RJ, Henrion M. Joint application of an empirical and mechanistic model for regional lake acidification. Environ Monit Assess 1995; 35:113-136. [PMID: 24202272 DOI: 10.1007/bf00633710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/1994] [Revised: 09/04/1994] [Indexed: 06/02/2023]
Abstract
The empirical direct distribution model for lake acidification is calibrated for use in an integrated assessment model which predicts the regional impact of an acid deposition control strategy. The calibration is based on the mechanistic Model of Acidification of Groundwater in Catchments (MAGIC). The models are applied jointly to a set of 33 statistically-selected lakes in the Adirondack region of New York. Calibration of the direct distribution model is based on a step-function application of acid deposition to MAGIC. Comparative evaluations of the resulting model predictions are made using historic deposition estimates and two alternative future deposition scenarios. The predictions of the direct distribution model match well the shapes and patterns of change of the regional distributions of ANC and pH predicted by MAGIC, the short- and medium-term dynamics of these changes, and the effect of including organic acids. However, small, long-term decreases in the fraction of incoming acid deposition neutralized by lakes and their watersheds predicted by MAGIC are not reproduced.
Collapse
Affiliation(s)
- M J Small
- Civil Engineering and Engineering and Public Policy, Carnegie Mellon University, 15213, Pittsburgh, PA, USA
| | | | | | | |
Collapse
|
31
|
Henrion M, Silva J. Cost savings from information technology in U.S. health care reform: insights from modeling. Healthc Inf Manage 1994; 8:23-8. [PMID: 10131848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- M Henrion
- Lumina Decision Systems, Inc., Palo Alto, CA
| | | |
Collapse
|
32
|
Pradhan M, Provan G, Henrion M. Experimental analysis of large belief networks for medical diagnosis. Proc Annu Symp Comput Appl Med Care 1994:775-9. [PMID: 7950030 PMCID: PMC2247817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present an experimental analysis of two parameters that are important in knowledge engineering for large belief networks. We conducted the experiments on a network derived from the Internist-1 medical knowledge base. In this network, a generalization of the noisy-OR gate is used to model causal independence for the multivalued variables, and leak probabilities are used to represent the nonspecified causes of intermediate states and findings. We study two network parameters, (1) the parameter governing the assignment of probability values to the network, and (2) the parameter denoting whether the network nodes represent variables with two or more than two values. The experimental results demonstrate that the binary simplification computes diagnoses with similar accuracy to the full multivalued network. We discuss the implications of these parameters, as well other network parameters, for knowledge engineering for medical applications.
Collapse
Affiliation(s)
- M Pradhan
- Institute of Decision Systems Research, Los Altos, CA 94022
| | | | | |
Collapse
|
33
|
Middleton B, Shwe MA, Heckerman DE, Henrion M, Horvitz EJ, Lehmann HP, Cooper GF. Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base. II. Evaluation of diagnostic performance. Methods Inf Med 1991; 30:256-67. [PMID: 1762579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have developed a probabilistic reformulation of the Quick Medical Reference (QMR) system. In Part I of this two-part series, we described a two-level, multiply connected belief-network representation of the QMR knowledge base and a simulation algorithm to perform probabilistic inference on the reformulated knowledge base. In Part II of this series, we report on an evaluation of the probabilistic QMR, in which we compare the performance of QMR to that of our probabilistic system on cases abstracted from continuing medical education materials from Scientific American Medicine. In addition, we analyze empirically several components of the probabilistic model and simulation algorithm.
Collapse
Affiliation(s)
- B Middleton
- Section on Medical Informatics, Stanford University, CA
| | | | | | | | | | | | | |
Collapse
|
34
|
Shwe MA, Middleton B, Heckerman DE, Henrion M, Horvitz EJ, Lehmann HP, Cooper GF. Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base. I. The probabilistic model and inference algorithms. Methods Inf Med 1991; 30:241-55. [PMID: 1762578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Part I of this two-part series, we report the design of a probabilistic reformulation of the Quick Medical Reference (QMR) diagnostic decision-support tool. We describe a two-level multiply connected belief-network representation of the QMR knowledge base of internal medicine. In the belief-network representation of the QMR knowledge base, we use probabilities derived from the QMR disease profiles, from QMR imports of findings, and from National Center for Health Statistics hospital-discharge statistics. We use a stochastic simulation algorithm for inference on the belief network. This algorithm computes estimates of the posterior marginal probabilities of diseases given a set of findings. In Part II of the series, we compare the performance of QMR to that of our probabilistic system on cases abstracted from continuing medical education materials from Scientific American Medicine. In addition, we analyze empirically several components of the probabilistic model and simulation algorithm.
Collapse
Affiliation(s)
- M A Shwe
- Section on Medical Informatics, Stanford University, CA
| | | | | | | | | | | | | |
Collapse
|
35
|
|